Polynucleotides and kits associated with soybean iron deficiency tolerance and methods of detection and breeding

Abstract

Molecular markers useful for identifying, selecting, and/or providing soybean plants displaying tolerance, improved tolerance, or susceptibility to iron deficiency, methods of their use, and compositions having one or more marker loci are provided. Methods comprise detecting at least one marker locus, detecting a haplotype, and/or detecting a marker profile. Methods may further comprise crossing a selected soybean plant with a second soybean plant. Isolated polynucleotides, primers, probes, kits, systems, as well as soybean plants, seeds, and parts thereof are also provided.

What is claimed is: 
     
       1. A method of detecting a first soybean plant or soybean germplasm with improved iron deficiency tolerance, the method comprising the steps of:
 (a) isolating nucleic acids from a population of soybean plants or soybean germplasm; 
 (b) detecting in the nucleic acids at least one favorable allele of one or more marker locus within a chromosomal interval flanked by and including Gm05:8808821-Gm05:9098413, wherein the one or more marker loci are selected from the group consisting of S29731 allele G, Gm05:9031274 allele G, Gm05:9032977 allele A, Gm05:9009488 allele G, Gm05:8897027 allele C, Gm05:8826919 allele T, Gm05:8912496 allele G, Gm05:8915863 allele C, Gm05:9011110 allele T, Gm05:9081402 allele G, Gm05:8912289 allele G, Gm05:8994830 allele C, Gm05:9098413 allele A, and Gm05:8808821 allele T; and 
 (c) selecting a first soybean plant based on the presence of the at least one favorable allele of the one or more marker locus; 
 (d) crossing the soybean plant selected in step (c) with a second plant not having said favorable allele of the one or more marker locus; 
 (e) collecting seeds from said cross; and 
 (f) growing a progeny soybean plant from said seed which comprises said favorable allele of the one or more marker locus, thereby producing a soybean plant with improved iron deficiency tolerance compared to a soybean plant not comprising said one or more markers in said chromosomal interval. 
 
     
     
       2. The method of  claim 1 , wherein said detecting comprises detection of a haplotype comprising marker S29731 allele G and a second marker selected from the group consisting of Gm05:9032977 allele A, Gm05:9009488 allele G, Gm05:8897027 allele C, Gm05:8826919 allele T, Gm05:8912496 allele G, Gm05:8915863 allele C, Gm05:9011110 allele T, Gm05:9081402 allele G, Gm05:8912289 allele G, Gm05:8994830 allele C, Gm05:8912456 allele T, Gm05:8826615 allele G, Gm05:8810680 allele C, Gm05:9098413 allele A, Gm05:8915641 allele T, Gm05:8912447 allele A, Gm05:8915642 allele A, Gm05:8915936 allele A, Gm05:8994518 allele A, Gm05:8911000 allele G, Gm05:8827043 allele C, Gm05:8808821 allele T, Gm05:8928168 allele C, Gm05:8913147 allele T, Gm05:9022152 allele A, Gm05:8822453 allele A, Gm05:8825498 allele C, Gm05:8814460 allele G, Gm05:8827199 allele C, Gm05:8827200 allele A, Gm05:8912397 allele T, Gm05:8809849 allele T, Gm05:8819720 allele T, Gm05:8826854 allele A, Gm05:8912668 allele C, Gm05:8818385 allele A, Gm05:8826076 allele G, Gm05:8913545 allele T, and Gm05:9080525 allele G. 
     
     
       3. The method of  claim 1 , wherein the detecting comprises amplifying the marker locus or a portion of the marker locus and detecting the resulting amplified marker amplicon. 
     
     
       4. The method of  claim 3 , wherein the amplifying comprises:
 a) admixing an amplification primer or amplification primer pair with a nucleic acid isolated from the first soybean plant or germplasm, wherein the primer or primer pair is complementary or partially complementary to at least a portion of the marker locus and is capable of initiating DNA polymerization by a DNA polymerase using the soybean nucleic acid as a template; and 
 b) extending the primer or primer pair in a DNA polymerization reaction comprising a DNA polymerase and a template nucleic acid to generate at least one amplicon. 
 
     
     
       5. The method of  claim 4 , wherein the admixing of step 1) further comprises admixing at least one nucleic acid probe. 
     
     
       6. The method of  claim 4 , wherein the detection comprises PCR analysis. 
     
     
       7. The method of  claim 1 , wherein the second soybean plant or soybean germplasm comprises an exotic soybean strain or an elite soybean strain.